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- PDB-5w0v: Crystal structure of full-length Kluyveromyces lactis Kap123 with... -

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Basic information

Entry
Database: PDB / ID: 5w0v
TitleCrystal structure of full-length Kluyveromyces lactis Kap123 with histone H4 1-34
Components
  • Histone H4 1-34
  • Kap123
KeywordsPROTEIN TRANSPORT / Budding yeast karyopherin / 23 HEAT repeats with a right-handed superhelical solenoid structure / Histone NLS recognition / The extra-long helix of the repeat 23
Function / homology
Function and homology information


HDMs demethylate histones / HATs acetylate histones / Condensation of Prophase Chromosomes / RNA polymerase I upstream activating factor complex / SUMOylation of chromatin organization proteins / replication fork protection complex / RMTs methylate histone arginines / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / small GTPase binding ...HDMs demethylate histones / HATs acetylate histones / Condensation of Prophase Chromosomes / RNA polymerase I upstream activating factor complex / SUMOylation of chromatin organization proteins / replication fork protection complex / RMTs methylate histone arginines / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / small GTPase binding / nucleosome assembly / protein import into nucleus / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / nucleus / cytoplasm
Similarity search - Function
Importin beta family / TOG domain / TOG / HEAT repeat / HEAT repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / HEAT repeat profile. ...Importin beta family / TOG domain / TOG / HEAT repeat / HEAT repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / HEAT repeat profile. / HEAT, type 2 / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Histone H4 / KLLA0E20769p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.821 Å
AuthorsAn, S. / Yoon, J. / Song, J.-J. / Cho, U.-S.
CitationJournal: Elife / Year: 2017
Title: Structure-based nuclear import mechanism of histones H3 and H4 mediated by Kap123.
Authors: An, S. / Yoon, J. / Kim, H. / Song, J.J. / Cho, U.S.
History
DepositionMay 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kap123
B: Kap123
C: Histone H4 1-34
D: Histone H4 1-34


Theoretical massNumber of molelcules
Total (without water)253,0124
Polymers253,0124
Non-polymers00
Water0
1
A: Kap123
C: Histone H4 1-34


Theoretical massNumber of molelcules
Total (without water)126,5062
Polymers126,5062
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kap123
D: Histone H4 1-34


Theoretical massNumber of molelcules
Total (without water)126,5062
Polymers126,5062
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.793, 87.697, 101.623
Angle α, β, γ (deg.)79.59, 81.45, 71.70
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Kap123


Mass: 122968.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CMF0
#2: Protein/peptide Histone H4 1-34


Mass: 3537.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Kluyveromyces lactis (yeast) / References: UniProt: P02309*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.76 % / Description: brick-shaped crystals
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate (pH 6.5), 0.2M sodium acetate, 30% PEG 4000 and 5% Jeffamin M-600

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.821→50 Å / Num. obs: 59828 / % possible obs: 98.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.045 / Net I/σ(I): 20.7
Reflection shellResolution: 2.821→2.93 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 5938 / Rpim(I) all: 0.479 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000HKL2000_v714-Linuxdata reduction
HKL-2000HKL2000_v714-Linuxdata scaling
Coot0.8.7model building
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VCH

5vch


Resolution: 2.821→33.787 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 1998 3.34 %
Rwork0.1702 --
obs0.1724 59760 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.821→33.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15749 0 0 0 15749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815983
X-RAY DIFFRACTIONf_angle_d1.03321679
X-RAY DIFFRACTIONf_dihedral_angle_d18.0669787
X-RAY DIFFRACTIONf_chiral_restr0.0572617
X-RAY DIFFRACTIONf_plane_restr0.0072779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8211-2.89160.35991300.29933762X-RAY DIFFRACTION91
2.8916-2.96970.34581430.26294145X-RAY DIFFRACTION98
2.9697-3.05710.3061440.23874149X-RAY DIFFRACTION99
3.0571-3.15570.31261440.23654164X-RAY DIFFRACTION99
3.1557-3.26840.30651440.22494153X-RAY DIFFRACTION99
3.2684-3.39910.33681420.20654119X-RAY DIFFRACTION99
3.3991-3.55370.25211440.18754152X-RAY DIFFRACTION99
3.5537-3.74080.25011440.17484178X-RAY DIFFRACTION99
3.7408-3.97480.20551440.16014150X-RAY DIFFRACTION99
3.9748-4.28120.22461430.14944144X-RAY DIFFRACTION99
4.2812-4.7110.21521440.13124180X-RAY DIFFRACTION99
4.711-5.39030.21031450.14964163X-RAY DIFFRACTION99
5.3903-6.78210.23951440.18894169X-RAY DIFFRACTION99
6.7821-33.78950.17851430.14154134X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.139-0.0362-0.00331.2897-0.53820.84550.03930.05630.04050.1619-0.05990.02320.09430.035700.6039-0.09060.00230.4441-0.01860.511797.7108-35.1684111.9119
20.4632-0.1201-0.37660.95010.58541.79540.09670.05180.07470.2115-0.04620.06120.08410.107300.5723-0.0493-0.02810.3849-0.01540.463687.2281-71.9745105.8846
30.121-0.1444-0.17990.08830.12680.21780.1453-0.0168-0.2447-0.3978-0.0882-0.38310.2520.1899-0.00010.87940.11540.03830.71610.08680.8332141.1256-76.025874.2367
40.619-0.6161-0.22111.0241-0.38040.1389-0.0391-0.0021-0.11580.30620.06490.03880.0836-0.079700.560.1248-0.05420.68850.05510.553121.9511-49.205480.7086
50.7410.2942-0.56660.6843-0.10621.6896-0.1750.00460.0101-0.09240.095-0.03720.08760.091700.34940.0182-0.01370.4653-0.01380.4204118.5218-26.335348.7681
62.0441-0.1331-1.65411.2151-0.66611.2911-0.16030.4731-0.11850.11630.16450.22390.1814-0.51110.09180.3519-0.0607-0.05380.7061-0.0080.505286.5551-29.040656.8974
70.040.05030.0120.06430.02060.0115-0.32320.03950.13540.0762-0.465-0.0904-0.16670.10310.00060.7660.0769-0.08621.05520.02220.786193.4516-57.9621123.1802
80.0163-0.0168-0.0120.02090.01740.0197-0.2627-0.0221-0.33640.1473-0.4175-0.15660.1192-0.0780.00180.90060.11880.09380.77150.02010.736117.3729-27.205551.1069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 588 )
2X-RAY DIFFRACTION2chain 'A' and (resid 589 through 1113 )
3X-RAY DIFFRACTION3chain 'B' and (resid 59 through 154 )
4X-RAY DIFFRACTION4chain 'B' and (resid 155 through 388 )
5X-RAY DIFFRACTION5chain 'B' and (resid 389 through 760 )
6X-RAY DIFFRACTION6chain 'B' and (resid 761 through 1112 )
7X-RAY DIFFRACTION7chain 'C' and (resid 13 through 19 )
8X-RAY DIFFRACTION8chain 'D' and (resid 14 through 19 )

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